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Yorodumi- PDB-8akc: Human Sirt6 in complex with ADP-ribose and fragment 3-(acetylamin... -
+Open data
-Basic information
Entry | Database: PDB / ID: 8akc | ||||||
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Title | Human Sirt6 in complex with ADP-ribose and fragment 3-(acetylamino)thiophene-2-carboxylic acid | ||||||
Components | NAD-dependent protein deacetylase sirtuin-6 | ||||||
Keywords | HYDROLASE / Deacylase / Fragment | ||||||
Function / homology | Function and homology information NAD-dependent histone H3K56 deacetylase activity / NAD-dependent histone H3K18 deacetylase activity / ketone biosynthetic process / NAD-dependent histone H3K9 deacetylase activity / protein delipidation / regulation of lipid catabolic process / NAD+- protein-lysine ADP-ribosyltransferase activity / NAD-dependent protein demyristoylase activity / NAD-dependent protein depalmitoylase activity / chromosome, subtelomeric region ...NAD-dependent histone H3K56 deacetylase activity / NAD-dependent histone H3K18 deacetylase activity / ketone biosynthetic process / NAD-dependent histone H3K9 deacetylase activity / protein delipidation / regulation of lipid catabolic process / NAD+- protein-lysine ADP-ribosyltransferase activity / NAD-dependent protein demyristoylase activity / NAD-dependent protein depalmitoylase activity / chromosome, subtelomeric region / pericentric heterochromatin formation / NAD+-protein-arginine ADP-ribosyltransferase activity / positive regulation of protein localization to chromatin / DNA damage sensor activity / positive regulation of stem cell differentiation / positive regulation of blood vessel branching / NAD-dependent protein lysine deacetylase activity / protein localization to site of double-strand break / retrotransposon silencing / protein acetyllysine N-acetyltransferase / cardiac muscle cell differentiation / NAD-dependent histone deacetylase activity / positive regulation of chondrocyte proliferation / positive regulation of telomere maintenance / protein deacetylation / negative regulation of glucose import / TORC2 complex binding / lncRNA binding / negative regulation of glycolytic process / negative regulation of protein localization to chromatin / DNA repair-dependent chromatin remodeling / positive regulation of double-strand break repair / positive regulation of vascular endothelial cell proliferation / negative regulation of gene expression, epigenetic / regulation of double-strand break repair via homologous recombination / negative regulation of protein import into nucleus / positive regulation of stem cell population maintenance / positive regulation of stem cell proliferation / regulation of protein secretion / negative regulation of transcription elongation by RNA polymerase II / site of DNA damage / NAD+-protein ADP-ribosyltransferase activity / negative regulation of cellular senescence / subtelomeric heterochromatin formation / regulation of lipid metabolic process / NAD+ ADP-ribosyltransferase activity / Transferases; Glycosyltransferases; Pentosyltransferases / nucleosome binding / NAD+ binding / positive regulation of fat cell differentiation / negative regulation of gluconeogenesis / pericentric heterochromatin / regulation of protein localization to plasma membrane / response to UV / Transferases; Acyltransferases; Transferring groups other than aminoacyl groups / nucleotidyltransferase activity / positive regulation of protein export from nucleus / determination of adult lifespan / circadian regulation of gene expression / base-excision repair / protein destabilization / regulation of circadian rhythm / positive regulation of insulin secretion / chromatin DNA binding / Pre-NOTCH Transcription and Translation / transcription corepressor activity / positive regulation of fibroblast proliferation / double-strand break repair / positive regulation of proteasomal ubiquitin-dependent protein catabolic process / glucose homeostasis / site of double-strand break / positive regulation of cold-induced thermogenesis / Processing of DNA double-strand break ends / damaged DNA binding / chromatin remodeling / negative regulation of cell population proliferation / intracellular membrane-bounded organelle / chromatin binding / chromatin / negative regulation of transcription by RNA polymerase II / endoplasmic reticulum / protein homodimerization activity / zinc ion binding / nucleoplasm / nucleus Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.83 Å | ||||||
Authors | You, W. / Steegborn, C. | ||||||
Funding support | Germany, 1items
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Citation | Journal: To Be Published Title: Development of novel Sirtuin 6 inhibitors and activators based on a protein crystallography-based fragment screen Authors: You, W. / Steegborn, C. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 8akc.cif.gz | 131.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb8akc.ent.gz | 99 KB | Display | PDB format |
PDBx/mmJSON format | 8akc.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ak/8akc ftp://data.pdbj.org/pub/pdb/validation_reports/ak/8akc | HTTPS FTP |
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-Related structure data
Related structure data | 8ak5C 8ak6C 8ak7C 8ak8C 8ak9C 8akaC 8akbC 8akdC 8akeC 8akfC 8akgC 8bl0C 8bl1C 8cnmC 8cnoC 5mf6S S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
-Assembly
Deposited unit |
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Unit cell |
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Noncrystallographic symmetry (NCS) | NCS domain:
NCS domain segments: Component-ID: 1 / Ens-ID: 1 / Beg auth comp-ID: LYS / Beg label comp-ID: LYS / End auth comp-ID: LEU / End label comp-ID: LEU / Refine code: 1 / Auth seq-ID: 15 - 297 / Label seq-ID: 9 - 291
NCS oper:
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-Components
-Protein , 1 types, 2 molecules AB
#1: Protein | Mass: 33631.594 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: SIRT6, SIR2L6 / Plasmid: pET151-D-TOPO / Production host: Escherichia coli (E. coli) / Strain (production host): Rosetta2 (DE3) pLysS References: UniProt: Q8N6T7, protein acetyllysine N-acetyltransferase |
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-Non-polymers , 7 types, 140 molecules
#2: Chemical | #3: Chemical | #4: Chemical | ChemComp-PEG / #5: Chemical | ChemComp-SO4 / #6: Chemical | #7: Chemical | #8: Water | ChemComp-HOH / | |
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-Details
Has ligand of interest | Y |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.6 Å3/Da / Density % sol: 52.8 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 5.7 Details: 1.6 M (NH4)2SO4, 10% PEG 400, and Bis-Tris buffer pH 5.7 PH range: 5.7-6.2 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N | |||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: BESSY / Beamline: 14.2 / Wavelength: 0.9184 Å | |||||||||||||||
Detector | Type: DECTRIS PILATUS 2M / Detector: PIXEL / Date: Sep 5, 2017 | |||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||||||||
Radiation wavelength | Wavelength: 0.9184 Å / Relative weight: 1 | |||||||||||||||
Reflection twin |
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Reflection | Resolution: 1.83→45.54 Å / Num. obs: 59281 / % possible obs: 99.9 % / Redundancy: 6.9 % / Biso Wilson estimate: 37.779 Å2 / CC1/2: 0.995 / Rrim(I) all: 0.17 / Net I/σ(I): 7.25 | |||||||||||||||
Reflection shell | Resolution: 1.83→1.94 Å / Redundancy: 7.2 % / Mean I/σ(I) obs: 0.82 / Num. unique obs: 9567 / CC1/2: 0.345 / Rrim(I) all: 2.01 / % possible all: 99.9 |
-Phasing
Phasing | Method: molecular replacement |
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 5MF6 Resolution: 1.83→45.54 Å / Cor.coef. Fo:Fc: 0.957 / Cor.coef. Fo:Fc free: 0.953 / SU B: 1.848 / SU ML: 0.06 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.026 / ESU R Free: 0.023 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 96.08 Å2 / Biso mean: 38.294 Å2 / Biso min: 19.64 Å2
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Refinement step | Cycle: final / Resolution: 1.83→45.54 Å
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Refine LS restraints |
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Refine LS restraints NCS | Number: 2145 / Type: TIGHT THERMAL / Rms dev position: 4.89 Å / Weight position: 0.5 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell | Resolution: 1.83→1.877 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
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